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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.30

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the bigbio/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.
        Report generated on 2025-08-09, 06:28 UTC based on data in: /home/runner/work/pmultiqc/pmultiqc/data

        bigbio/quantms Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/bigbio/quantms

        Methods

        Data was processed using bigbio/quantms v1.5.0 (doi: 10.5281/zenodo.7754148) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v24.10.5 (Di Tommaso et al., 2017) with the following command:

        nextflow run bigbio/quantms -profile docker --custom_config_base /home/yueqx/Data_Disk/proteogenomics/quantms/test_dia/confs -c /home/yueqx/Data_Disk/proteogenomics/quantms/test_dia/confs/run_latest_dia.config

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        ASSEMBLE_EMPIRICAL_LIBRARYDIA-NN2.1.0
        CONVERT_RESULTSquantms-utils0.0.23
        FINAL_QUANTIFICATIONDIA-NN2.1.0
        GENERATE_CFGquantms-utils0.0.23
        INDIVIDUAL_ANALYSISDIA-NN2.1.0
        MSSTATS_LFQbioconductor-msstats4.14.0
        r-base4.4.2
        MZML_STATISTICSquantms-utils0.0.23
        PRELIMINARY_ANALYSISDIA-NN2.1.0
        SAMPLESHEET_CHECKquantms-utils0.0.23
        SDRF_PARSINGsdrf-pipelines0.0.32
        THERMORAWFILEPARSERThermoRawFileParser1.3.4
        WorkflowNextflow24.10.5
        bigbio/quantmsv1.5.0

        bigbio/quantms Workflow Summary

        Input/output options

        export_decoy_psm
        true
        input
        /home/yueqx/Data_Disk/proteogenomics/quantms/test_dia/PXD026600.sdrf.tsv
        outdir
        /home/yueqx/Data_Disk/proteogenomics/quantms/results_dia

        SDRF validation

        skip_factor_validation
        true
        use_ols_cache_only
        true
        validate_ontologies
        true

        Protein database

        database
        /home/yueqx/Data_Disk/proteogenomics/quantms/test_dia/REF_EColi_K12_UPS1_combined.fasta

        Database search

        allowed_missed_cleavages
        1
        max_fr_mz
        1500
        max_mods
        2
        max_peptide_length
        30
        max_pr_mz
        950
        max_precursor_charge
        3
        min_fr_mz
        500
        min_peptide_length
        15
        min_pr_mz
        350

        Modification localization

        luciphor_debug
        0

        PSM re-scoring (general)

        run_fdr_cutoff
        0.10

        PSM re-scoring (Percolator)

        description_correct_features
        0

        Consensus ID

        consensusid_considered_top_hits
        0
        min_consensus_support
        0

        Isobaric analyzer

        quant_activation_method
        HCD

        Protein Quantification (LFQ)

        feature_with_id_min_score
        0.10

        DIA-NN

        diann_normalize
        false

        Statistical post-processing

        contrasts
        pairwise

        Quality control

        enable_pmultiqc
        true
        pmultiqc_idxml_skip
        true

        Institutional config options

        custom_config_base
        /home/yueqx/Data_Disk/proteogenomics/quantms/test_dia/confs

        Generic options

        publish_dir_mode
        symlink
        trace_report_suffix
        2025-07-22_10-44-58

        Core Nextflow options

        configFiles
        N/A
        container
        [withLabel:diann:docker.io/library/diann-2.1.0]
        containerEngine
        docker
        launchDir
        /home/yueqx/Data_Disk/proteogenomics/quantms
        profile
        docker
        projectDir
        /home/yueqx/Data_Disk/proteogenomics/quantms/bigbio/quantms
        runName
        loquacious_wilson
        userName
        yueqx
        workDir
        /home/yueqx/Data_Disk/proteogenomics/quantms/work

        MultiQC v1.30 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.